- ChimeraX-users - RBVI Mailing Lists

Re: Command line interface saving
by Mark Rosenberg 26 Aug '24

26 Aug '24

Thanks, Guillaume, for the excellent service. I found the log window now. I cannot cycle through my previous commands, though; in the bottom window, “command:’ with the down and up arrow. Is there a way to import those, please? Many thanks Mark mjfssmr mark.rosenberg(a)manchester.ac.uk<mailto:mark.rosenberg@manchester.ac.uk> mjfssmr mark.rosenberg(a)manchester.ac.uk<mailto:mark.rosenberg@manchester.ac.uk>mjfssmr mark.rosenberg(a)manchester.ac.uk On 26 Aug 2024, at 12:46, mjfssmr <http://mark.rosenberg@manchester.ac.uk> wrote: Thanks, Guillaume, for the excellent service. I found the log window now. I cannot cycle through my previous commands, though; in the bottom window, “command:’ with the down and up arrow. Is there a way to import those, please? Many thanks Mark mjfssmr mark.rosenberg(a)manchester.ac.uk mjfssmr mark.rosenberg(a)manchester.ac.uk On 26 Aug 2024, at 12:31, Guillaume Gaullier <http://guillaume.gaullier@KEMI.UU.SE> wrote: Hello, The log of your saved session should be there, but it is hidden at the top of the log window when you re-open the session file. There should be a black triangle that you can click to open the log contents from the previous session. I hope this helps, Guillaume ________________________________ From: Mark Rosenberg via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: Monday, August 26, 2024 1:26:25 PM To: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Command line interface saving Hi If I save my session in .cxs format, move to another machine, and open the same session again, I “lose" my commands. The commands don’t appear to be saved. How do I remedy this, please? Thanks Mark VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ [http://uu.se<https://urldefense.com/v3/__http://www.uu.se/om-uu/dataskydd-personuppgifte…> E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy [http://uu.se<https://urldefense.com/v3/__http://www.uu.se/en/about-uu/data-protection-po…>

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Re: Command line interface saving
by Guillaume Gaullier 26 Aug '24

26 Aug '24

Not that I know, sorry. But maybe somebody else knows, so it is better to keep the list in CC. 😊 Cheers, Guillaume ________________________________ From: Mark Rosenberg <mark.rosenberg(a)manchester.ac.uk> Sent: Monday, August 26, 2024 1:46:29 PM To: Guillaume Gaullier Subject: Re: Command line interface saving Thanks, Guillaume, for the excellent service. I found the log window now. I cannot cycle through my previous commands, though; in the bottom window, “command:’ with the down and up arrow. Is there a way to import those, please? Many thanks Mark mjfssmr mark.rosenberg(a)manchester.ac.uk mjfssmr mark.rosenberg(a)manchester.ac.uk On 26 Aug 2024, at 12:31, Guillaume Gaullier <guillaume.gaullier(a)KEMI.UU.SE> wrote: Hello, The log of your saved session should be there, but it is hidden at the top of the log window when you re-open the session file. There should be a black triangle that you can click to open the log contents from the previous session. I hope this helps, Guillaume ________________________________ From: Mark Rosenberg via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: Monday, August 26, 2024 1:26:25 PM To: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Command line interface saving Hi If I save my session in .cxs format, move to another machine, and open the same session again, I “lose" my commands. The commands don’t appear to be saved. How do I remedy this, please? Thanks Mark VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ [uu.se]<https://urldefense.com/v3/__http://www.uu.se/om-uu/dataskydd-personuppgifte…> E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy [uu.se]<https://urldefense.com/v3/__http://www.uu.se/en/about-uu/data-protection-po…> VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.

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Command line interface saving
by Mark Rosenberg 26 Aug '24

26 Aug '24

Hi If I save my session in .cxs format, move to another machine, and open the same session again, I “lose" my commands. The commands don’t appear to be saved. How do I remedy this, please? Thanks Mark

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molmap command question
by Grigory Mechetin, Ph.D. 23 Aug '24

23 Aug '24

Dear ChimeraX developers, when I use the molmap command on grid ('molmap #1 10 onGrid #2', grid2 was created with' vop new size 256,256,256 gridSpacing 0.74' command ) I get half-map. How to get the full one? When I use molmap without onGrid it generates the volume with non-equal grid size, but I need square 256^3 grid. [cid:3853c8fe-0ccd-4133-ba08-4732e3be8905] Best regards, Grigory Mechetin, PhD, MEMS, Duke University.

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Data handling / privacy policy information?
by Frumolt, Brian 23 Aug '24

23 Aug '24

Hi, We are looking at ChimeraX for commercial use. I was looking on the site for information related to data use and privacy policies. I understand the app runs locally, but was wondering whether it leverages any web services, or passes any data outside the local installation? We have strict data handling policies in place for our clients, so would need to be aware. If there is a policy document I missed, that would be ideal. Thanks! Brian This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying, or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently delete the original and any copies of this email and any attachments thereto.

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Morphing two GPCR conformations
by Enrico Martinez 23 Aug '24

23 Aug '24

Dear Chimera-X users! I try to use the morph command to model the conformational change of GPCR related to its activation. Having two superimposed conformations of the receptor, which are different in the position of the internal part of the transmembrane helix VI, I try to visualize the displacement of this helix using morph #2,1 frames 250 Unfortunately the produced trajectory looks very unnatural (one helix overlaps with another one). Would it be possible to improve the accuracy of such morphing e.g. providing some restraints? Many thanks in advance ! Enrico

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Mol 2.0 desktop version
by Nicholas Koylass 22 Aug '24

22 Aug '24

Good day, I am trying to interface ChimeraX with a XML file that was converted to json to perform MOLE Channel Coloring by Property. However, I did not use the mole server. I used the desktop version since the server was unavailable. Thus, I received this error : molepore-7sqf.json does not look like Mole Online json file, does not contain Channels. Can anyone assist me with this? Thanks, Respectfully, Nicholas Nicholas Koylass Ph.D. Candidate, Department of Physiology, Qiu Lab XDBio Graduate Program Johns Hopkins School of Medicine nkoylas1(a)jh.edu

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Restoration of missing helical fragments of the structure
by Enrico Martinez 22 Aug '24

22 Aug '24

Dear Chimera-X users ! Suppose I have a pdb structure with a missed C-terminal fragment corresponding to the transmembrane helical part that should anchor the protein in the membrane. Is it possible to use some built-in utilities (modeller?) to predict this missing fragment based on the full length sequence of the entire construct? Many thanks in advance Enrico

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results swiss dock
by Aurélie Hoeffel 21 Aug '24

21 Aug '24

Dear Chimeras members, I obtained some docking results from swiss dock, unfortunately my result.dock4 document is not readable in chimerax, I did not achieve to open it. Is it something special I have to do? Because, on the website it is written that we can directly upload it and it will work but for me chimerax did not recognize my .dock4 document. What should I do? Thank for the answer, Aurelie Hoeffel

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ChimeraX docker arm64
by Daniel Diaz 20 Aug '24

20 Aug '24

We are unable to install chimerax in our ubuntu 22.04 docker image when running on arm64 architecture. We use it to add hydrogen atoms to our cif files for our protein ML data engineering pipelines. We are trying to scale our dataset generation pipeline to the new cluster on TACC (vista) which has arm64 chips. We are running it in a singularity container, which I create by converting my docker image, and I am unable to build the docker image using arm64. How do you recommend we proceed? Here is the error stack: $ apt-get update --fix-missing && apt-get install -y /dependencies/chimerax-daily.deb Hit:1 http://ports.ubuntu.com/ubuntu-ports jammy InRelease Hit:2 http://ports.ubuntu.com/ubuntu-ports jammy-updates InRelease Hit:3 http://ports.ubuntu.com/ubuntu-ports jammy-backports InRelease Hit:4 http://ports.ubuntu.com/ubuntu-ports jammy-security InRelease Reading package lists... Done Reading package lists... Done Building dependency tree... Done Reading state information... Done Note, selecting 'ucsf-chimerax-daily:amd64' instead of '/dependencies/chimerax-daily.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: ucsf-chimerax-daily:amd64 : Depends: libasound2:amd64 but it is not installable Depends: libatk1.0-0:amd64 but it is not installable Depends: libbz2-1.0:amd64 but it is not installable Depends: libc6:amd64 but it is not installable Depends: libcairo-gobject2:amd64 but it is not installable Depends: libcairo2:amd64 but it is not installable Depends: libcrypt1:amd64 but it is not installable Depends: libcups2:amd64 but it is not installable Depends: libdbus-1-3:amd64 but it is not installable Depends: libdrm2:amd64 but it is not installable Depends: libegl1:amd64 but it is not installable Depends: libexpat1:amd64 but it is not installable Depends: libffi7:amd64 but it is not installable Depends: libfftw3-single3:amd64 but it is not installable Depends: libfontconfig1:amd64 but it is not installable Depends: libfreetype6:amd64 but it is not installable Depends: libgcc-s1:amd64 but it is not installable Depends: libgdk-pixbuf2.0-0:amd64 but it is not installable Depends: libgfortran5:amd64 but it is not installable Depends: libgl1:amd64 but it is not installable Depends: libglib2.0-0:amd64 but it is not installable Depends: libglu1-mesa:amd64 but it is not installable Depends: libgstreamer-plugins-base1.0-0:amd64 but it is not installable Depends: libgstreamer1.0-0:amd64 but it is not installable Depends: libgtk-3-0:amd64 but it is not installable Depends: liblzma5:amd64 but it is not installable Depends: libncursesw6:amd64 but it is not installable Depends: libnspr4:amd64 but it is not installable Depends: libnss3:amd64 but it is not installable Depends: libopenjp2-7:amd64 but it is not installable Depends: libosmesa6:amd64 but it is not installable Depends: libpango-1.0-0:amd64 but it is not installable Depends: libpangocairo-1.0-0:amd64 but it is not installable Depends: libpulse-mainloop-glib0:amd64 but it is not installable Depends: libpulse0:amd64 but it is not installable Depends: libsqlite3-0:amd64 but it is not installable Depends: libssl3:amd64 but it is not installable Depends: libstdc++6:amd64 but it is not installable Depends: libtinfo6:amd64 but it is not installable Depends: libuuid1:amd64 but it is not installable Depends: libwayland-client0:amd64 but it is not installable Depends: libwayland-cursor0:amd64 but it is not installable Depends: libwayland-egl1:amd64 but it is not installable Depends: libwayland-server0:amd64 but it is not installable Depends: libx11-6:amd64 but it is not installable Depends: libx11-xcb1:amd64 but it is not installable Depends: libxcb-glx0:amd64 but it is not installable Depends: libxcb-icccm4:amd64 but it is not installable Depends: libxcb-image0:amd64 but it is not installable Depends: libxcb-keysyms1:amd64 but it is not installable Depends: libxcb-render-util0:amd64 but it is not installable Depends: libxcb-util1:amd64 but it is not installable Depends: libxcb-xinerama0:amd64 but it is not installable Depends: libxcb1:amd64 but it is not installable Depends: libxcomposite1:amd64 but it is not installable Depends: libxcursor1:amd64 but it is not installable Depends: libxdamage1:amd64 but it is not installable Depends: libxext6:amd64 but it is not installable Depends: libxfixes3:amd64 but it is not installable Depends: libxi6:amd64 but it is not installable Depends: libxkbcommon0:amd64 but it is not installable Depends: libxkbcommon-x11-0:amd64 but it is not installable Depends: libxrender1:amd64 but it is not installable Depends: libxtst6:amd64 but it is not installable Depends: zlib1g:amd64 but it is not installable E: Unable to correct problems, you have held broken packages. -- Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin

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Protein backbone representation
by Alex Henley 20 Aug '24

20 Aug '24

I was wondering how I can achieve this structure representation. The papers I read cite Chimera, but I cannot figure it out. Any help is appreciated.

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Per-Model Lighting Options
by ygilron＠asu.edu 20 Aug '24

20 Aug '24

I am trying to render different parts of my model in different styles. This is done to emphasize changes in a ligand's force field between different simulations. I would like every part of my model to be rendered in "full", and only change the style for my ligand so it will appear either as "flat", with or without a "silhouettes" toggled on. Is there an option to do this? I would like to just render my custom residue "DIO" in the "flat" style. As you can see from the output it is part of chain 1: " ...Non-standard residues in dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 DIO — (DIO) ..." I tried to use the following command to separately render different parts of a chain: lighting model #1:DIO flat from the console: >lighting modell #1:DIO flat Expected a keyword while selecting DIO fro the select menu and then running : lighting flat changes the style on the whole image. P.S. full output command when I loaded the molecule: open .\dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb" format pdb coordsets true Summary of feedback from opening C:\Users\yis\Desktop\Wenwei Lab\article\first_draft_figs\dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb warnings Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV ... 1997 messages similar to the above omitted dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb title: PH06_elaxed_rank_001_alphafold2_translated_100_xyz.pdbqt in water t= 0.00000 step= 0 [more info...] Chain information for dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 Chain Description ? No description available Non-standard residues in dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 DIO — (DIO) FE2 — (FE2) dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb has 1001 coordinate sets

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Thanks Elaine, Tom, Eric and team
by Artie Kushner 20 Aug '24

20 Aug '24

Apologies for an off-topic message. I'd like to express my gratitude to Elaine Meng in particular and the rest of the RVBI team who are tirelessly killing it in the Users mailing list with questions. On top of the amazing software, I appreciate the consistency, informativeness and thoughtfulness of each individual response. I learn a lot about ChimeraX and the community by reading other people's questions and answers. Thanks and kind regards from BC and Manitoba, Canada Artem

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Assistance Required: Visualizing Complete Amino Acid Residue with Cartoon Transparency in ChimeraX
by Amandeep Sharma (P24BB0001) 19 Aug '24

19 Aug '24

Dear ChimeraX users, I am reaching out for assistance with visualizing amino acid residues in ChimeraX, particularly when part of the residue is embedded within a cartoon structure representation. I am aiming to achieve a visualization similar to what is possible in PyMOL, where the complete residue is visible even when it intersects with other structural elements and adjust the transparency of the cartoon representation so that the embedded atoms of the residue can be clearly seen. I am struggling to get the desired result. To provide context and illustrate the issue, I am enclosing images of the current visualization: - *Image 1:* Shows the current state where part of the residue is obscured by the cartoon structure. - *Image 2:* Demonstrates the desired outcome where the residue is fully visible, including the embedded atoms. I am looking for a solution that combines the aspects seen in the two attached images, allowing for clear visualization of the residue and improved transparency. Thank you very much for your assistance. I look forward to your guidance on how to achieve this in ChimeraX. Best regards, Amandeep -- Amandeep Sharma PhD Student (2024-25) Dept. of Bioscience & Bioengineering Indian Institute of Technology Jodhpur Karwar 342037, Rajasthan

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Alligning a trajectory
by ygilron＠asu.edu 19 Aug '24

19 Aug '24

Hi I am new to UCSF ChimeraX, and would like to learn how to use it for visualizing trajectories. Previously, I was using pymol for this, but would like to use ChimeraX's better image rendering for a publication. I was able to load the .pdb file of my trajectory with: open <"path/to/pdb"> format pdb coord T Currently, this is the info of my file: >info 1 models #1, lambda25_trajectory_1k_res.pdb, shown 8094 atoms, 8219 bonds, 514 residues, 1 chains ( ), 100 coordsets I would like to remove translations and rotations by fitting each frame with a command similar to 'align': align matchatoms toAtoms refatoms [ cutoffDistance d ] [ move what ] [ each level ] [ reportMatrix true | false ] pairing-options Although, it seems I would have to do this manually 99 times for each pair of coordsets of the trajectory. Additionally, I am not sure I have the correct syntax for choosing a coordset from a model: align #1 , 1 toAtoms #1 ,2 gave me the following output: align #1 , 1 toAtoms #1 ,2RMSD between 8094 atom pairs is 0.000 angstroms That probably shouldn't be that accurate, right? In PyMOL one would use the command: intra_fit <model name> in order to do this. The best I was able to deduce was the following command: coordset #1 1,100 holdSteady @ca I am not sure if this is doing the same thing (rmsd fitting of model #1 coordset 1 to model #1 coordset 2.... ....model #1 coordset 99 to model #1 coordset 100 ) but rather just fixing the C-alpha atoms in place? is this equivalent? Also, I noticed this only aligns the coordsets once, and then reverts back to the default trajectory of tumbling around with all the rotations and translations. How can I set this holdSteady to be permanent for all future plays of my trajectory? Best, Yishai

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2D labels colored by chain color
by NG, Cheukhei Jackie [Student] 19 Aug '24

19 Aug '24

Dear sir/madam, I am trying to generate publication-quality images with chimeraX with appropriate 2D labels. 1. Is there a variable I could use to represent the coloring of my current chain so i can apply in the command where the selection is multiple chains: label sel color (the variable)? 2. is the an offset parameter or any relevant parameters in the 2D label command that are recommended for publication use? Thank you very much for your time. Thanks, Jackie [https://www.polyu.edu.hk/emaildisclaimer/PolyU_Email_Signature.jpg] Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.

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Feature of chimera
by Arpita Nandy 19 Aug '24

19 Aug '24

Hi, I am a PhD student from Germany and would like to make a figure where I can highlight specific proteins of interest in the mitoribosome complex of yeast. Could you please assist me to use ChimeraX in this context. Best regards Arpita Nandy

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Usage and Distribution of ChimeraX at our Upcoming Max Planck Institute Summer School
by SantaLucia, Daniel 15 Aug '24

15 Aug '24

Hello ChimeraX team, My name is Dan SantaLucia; I'm a research scientist working under Prof. Frank Neese and Prof. Serena DeBeer at the Max Planck Institute for Chemical Energy Conversion. One thing we do every year is to organize a summer school for students from all over the world, where they get to learn in-depth about many different spectroscopic techniques as well as quantum chemical calculations to help them in their interpretations of these datasets. You can find more information here, if you're curious: https://summerschool.cec.mpg.de/en/home thing that would be really nice would be to offer students the ability to use ChimeraX alongside our tutorial/practical sessions. We use ORCA to do calculations (considering, of course, that Frank invented it), and we've found that ChimeraX has a lot of really nice features that would be perfect for helping the students to learn. What I wanted to ask was this: do we have permission to distribute the download files at: https://www.rbvi.ucsf.edu/chimerax/download.html to the students? They would be distributed on flash drives that we give to the students, and we would distribute the Windows, Mac, and Linux versions so that we could cover all users. The internet connection is not the best, unfortunately, at our venue, which is why they can't just go to the link to download it themselves. To be clear: this is a non-commercial use event, where we simply have international students coming to attend the summer school, and this is an event that is for learning purposes only. Nonetheless, I want to have your explicit permission for distribution of ChimeraX to the students as well as your permission for them to use your software at our summer school? Thanks so much, and looking forward to hearing back from you, -Dan [1668779311055] [1668779979115] Dr. Daniel J. SantaLucia MPI-KoFo/CEC Joint Workspace Stiftstraße 34-36 45470 Mülheim an der Ruhr Germany Tel.: +49 208 306 3724

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problem to open a swiss dock results file
by Aurélie Hoeffel 13 Aug '24

13 Aug '24

Dear Chimeras members, I would be interested to use chimera x for interpreting some results of my docking. I precise it is the first time I use swiss dock as well as chimera x, after receiving the swiss dock file in a tar.gz format, I compress it via 7Zip but then chimera x, is not able to process and open my document, ii is just written, tar data ,Unrecognized file suffix '.tar', so I do not kwo if the pb come from chimera or swiss dock, do you know how I can solve the problem? Thanks in advance, Aurelie

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ChimeraX-daily (1.9, 5 Aug 2024); Log panel stealing focus
by leeyang+chimerax＠gmail.com 10 Aug '24

10 Aug '24

Hi, Downloaded the above Daily (macOS 14.5, Universal), primarily for the workaround retrieving mmCIFs containing an underscore (#15557). I noticed that the Log toolpanel steals focus whenever it updates. Perhaps something that has already been dealt with? Otherwise, thought I should post it here. Cheers, Yang

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AlphaFold version in ChimeraX 1.8
by Anna Mestre Borras 09 Aug '24

09 Aug '24

Hi, I would like to confirm which is the AlphaFold version in ChimeraX 1.8 when using Tools --> structure prediction --> AlphaFold. Thanks! Best, Anna

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Could not display the lipid such as cardiolipin
by 杨雪梅 08 Aug '24

08 Aug '24

Dear ChimeraX support group, When I open my PDB with ChimeraX, some lipids (get from the coot library with three-code) could not be seen. When it open with pymol, the lipids were displayed normal. Have you met such problem and how did you fix it? Looking forward to your kind help. Sincerely yours, Xuemei Yang Chinese Academy of Sciences Shanghai Institute of Materia Medica

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Could not display the lipid such as cardiolipin
by Yang Xuemei 08 Aug '24

08 Aug '24

Dear ChimeraX support group, When I open my PDB with ChimeraX, some lipids (get from the coot library with three-code) could not be seen. When it open with pymol, the lipids were displayed normal. Have you met such problem and how did you fix it? Looking forward to your kind help. Sincerely yours, Xuemei Yang Fudan University Chinese Academy of Sciences Shanghai Institute of Materia Medica

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problem for the PDB deposition
by Yanhe Zhao 07 Aug '24

07 Aug '24

Dear ChimeraX community and developer, I am trying to deposit my map with model. I save the model from pdb to cif in ChimeraX because of large amount of atoms, then got error as "Missing '_entity_poly.pdbx_strand_id' item. I tired to use pymol to open my pdb and save it as cif by 'Export Molecule', in which I just use the default options. I checked the saved cif in ChimeraX, which is weird since it couldn't be show in cartoon style. Is there any easy to handle this in ChimeraX or any option should be used in the 'Export Molecule' in Pymol? Thanks and cheers, Yanhe

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Inverted fit in map ?
by GOVAERTS Cédric 07 Aug '24

07 Aug '24

Hi Team I would like to compare to conformations of a protein whose structures have been solved by cryoEM (conf1 with map1 and conf2 with map2) So I want to have the coordinates *and* the cryoEM maps aligned. Aligning the two conformations is easy thanks to matchmaker (align conf1 to conf2) However, I can I align map2 onto conf2 so that I can compare with map1 ? Basically I would like to do an “inverse” fit into map conf2->map2. Can I do that ? Note : I do not want to align map2 ontomap1 because of resolution and structural differences, the superimposition should be done at the coordinate level (actually on a subset of it which is easy in matchmaker). Thanks ! Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77<tel:+3226505377> Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

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Question regarding per-Residue RMSD
by Zimiao Meng 07 Aug '24

07 Aug '24

Dear Developers/Researchers of ChimeraX, I'm a student researcher trying to utilize ChimeraX to analyze structures of models predicted by programs. Currently, when I do matchmaker, only the RMSD value is displayed. I'd like to know the per-residue RMSD (which should also be the alignment error for that residue) for a section of the sequence that's a few hundred residues long. I wonder if there is a way to display the information that ChimeraX used to calculate the overall RMSD? Or would the only way to do it be writing a python script? Best, Zimiao

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Looking for scale
by David S. Fay 07 Aug '24

07 Aug '24

Hi, Does anyone know if a reference-type PAE bar exists for the ChimeraX PAE plot when using the Rainbow (orange/yellow/blue) selection? Something similar to what AF provides for the (green) scale (below) or the electro-charge (blue/white/red) maps? Rainbow provides a nice visual range, but I couldn't find an associated score reference. [cid:7001d3eb-43d0-4009-9596-6843ea44695a@namprd05.prod.outlook.com] Thanks, David

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ChimeraX website not accessible from time to time
by Roden Deng Luo 07 Aug '24

07 Aug '24

Hi, This has happened quite some times in the last few months. I realized just now that I could not access https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/core/logger.html. I then checked the following, and all were not working. Is this my own problem or a server-side issue? Is there an offline developer documentation (PDF or HTML)? https://www.cgl.ucsf.edu/chimerax/docs/user/commands/log.html https://www.cgl.ucsf.edu/chimerax/download.html https://www.cgl.ucsf.edu/chimerax/docs/licensing.html Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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PhenixUI Installation Errors
by Caballero Silva, Guillermo 06 Aug '24

06 Aug '24

Good afternoon, I am a current postdoctoral fellow working primarily with low resolution (4-6A) CryoEM Data/Models and recently discovered the "Local EM Fitting Tool" described in https://doi.org/10.1101/2024.05.16.594509 which I believe will help me overcome some of the issues I am currently experiencing in model docking/building. I am currently running ChimeraX version 1.5 and Phenix-1.20.1-4487 and have been trying to install PhenixUI from ChimeraX "More Tools" but have not been able to. I have tried installing older version of PhenixUI but was only able to install PhenixUI version 1.0.5. When I try to upgrade to the current version I am received with the following message: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\gcaballe\downloads\chimerax_phenixui-1.2.2-py3-none-any.whl Requirement already satisfied: ChimeraX-MapData~=2.0 in c:\users\gcaballe\documents\chimerax\bin\lib\site-packages (from ChimeraX-PhenixUI==1.2.2) (2.0) ERROR: Could not find a version that satisfies the requirement ChimeraX-Map~=1.1.3 (from chimerax-phenixui) (from versions: none) ERROR: No matching distribution found for ChimeraX-Map~=1.1.3 [notice] A new release of pip available: 22.2.2 -> 24.2 [notice] To update, run: C:\Users\gcaballe\Documents\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip It is my understanding that I need to install "ChimeraX-Map~=1.1.3" but cannot find how/where to do so. My current OS is Windows x64. Is it possible to install Local EM Fitting with my current set up or do I need to do any changes modifications. Please let me know if there is any more information I can provide and thank you in advance for your help and support. Kind regards, Guillermo Caballero Silva Postdoctoral Fellow Amgen Canada [cid:image001.png@01DAE4FC.105C31E0]

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Doubt about "contacts" command in ChimeraX
by Manuel Ospina 05 Aug '24

05 Aug '24

Good evening, I am actually using ChimeraX and I am trying to figure out a command that can show me all the contacts of my ligand below 3.0A with my protein. Unfortunately, I have not found anything clear enough to do so. Is there a way to do this? Another doubt is, if I have labelled 2 contacts (i.e 2.576A and 3.149A) but I am interested in only showing the label " 2.576A", I try deleting the other contact label (" 3.149A") by selecting it and typing the "label del" command, but this will delete my label of interest as well. Is there a way of only deleting specific labels from the contacts? Any help is appreciated. Best regards, Manuel

3 3

Silhoutte
by Shubhangi Agarwal 05 Aug '24

05 Aug '24

Dear developers, I am trying to outline surfacerepresentation of my protein structure with the silhouette feature but it gives me black dashes along rest of the surface which I don’t want, how can I just use the black borderline feature for my surface and protein? Figure attached below. Thank you Shubhangi [cid:922B93FD-C686-4CED-8281-EFF2FAFC08D2]

3 5

2D PAE plot with colored PAE domains
by David S. Fay 05 Aug '24

05 Aug '24

Hi All, Was trying to get the ChimeraX 2D PAE plot to display the colored PAE domains consistent with the ribbon diagram. The button “Color PAE Domains” colors the ribbon diagram by coherent domains, but the 2D plot is still colored by PAE (error). The Meng et al., 2023 has nice examples of this (e.g., 1f) coloring. Thanks in advance! David

2 1

save images
by Aritz Roa Eguiara 02 Aug '24

02 Aug '24

Dear Sir or Madam, I am trying to make a default .cxc file that I can use to automatically save the view for publication. I am using the following: save /path/image.tiff pixelSize 0.05 supersample 4 This turned out to give me the best files for most cases, but depending on the zoom I get different file sizes. Is there any way to have a standard command that gives me high quality images and that always have the same dimensions regardless of the zoom? I understand that the issue comes from the different pixel size of the zoom and that I am specifying a pixel size on the command, but when trying other alternatives I have not been successful to get proper images... All the best, Aritz

3 2

August 1 Chimera(X) website downtime
by Elaine Meng 01 Aug '24

01 Aug '24

Planned downtime for server maintenance: The Chimera and ChimeraX websites, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable August 1, 3-6 pm PDT. Apologies for any inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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PDB search in ChimeraX
by Enrico Martinez 01 Aug '24

01 Aug '24

Dear ChimeraX users, I have a pdb structure of membrane protein without any information about it. Is it possible to use some chimera-X tool to identify the name of this protein and find its pdb code in pdb database ? Many thanks in advance Enrico

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seeking AlphaFold advice
by Elaine Meng 30 Jul '24

30 Jul '24

Hi David, Please send questions to the chimerax-users address CC'd here instead of to me individually. I am not an AlphaFold expert, whereas maybe others on the list can answer your questions. I removed your link because I didn't know if you were willing to share it publicly. If so, please repost to the group (chimerax-users address CC'd here). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 30, 2024, at 6:26 AM, David S. Fay <DavidFay(a)uwyo.edu> wrote: > > Thanks for that information Elaine. That is my take as well, but I know much less about these things… > > On a slightly different note, I really wish there was an alphafold “best practices” tutorial or methods paper. Mainly I’m focused on protein-protein interactions, which is something I think many people are interested in. I gave a talk to my department recently, where I tried to do some of this. But because this isn’t my area, I rather feel like this is a case of the slightly blind leading the even-more blind. Still, I’ve attached a link to a google folder that contains my talk. I’d love to get feedback on this from experts in the field, such as folks at ChimeraX. > > And one last question, which you might have an opinion about. Is AF3 any good at predicted changes in structure with amino acid substitutions? I know that AF2 was not, but given that AF3 includes secondary modifications, it would seem like this capability should be improved? Especially if it’s relying less on MSAs. For that matter, do the folks at ChimeraX have an opinion about how AF3 alters structure and interactions based on modifications like phosphorylation? > > Thanks, > > David

2 1

Hide axis indicator
by Hantz, Eric 30 Jul '24

30 Jul '24

Hello, I am using ChimeraX 1.8 macOS, and I am having trouble finding a way to hide the axes indicator. I am trying to make a figure of a ligand bound protein structure with the electron density shown for the ligand. The best I can have been able to do is make the axes indicator slightly transparent but it is still visible. Thanks, Eric

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Re: Answer to question regarding Consurf and ChimeraX
by Elaine Meng 29 Jul '24

29 Jul '24

Hi David, There is no option to call the ConSurf web service from inside ChimeraX (or Chimera), I just meant to ask whether you could display the output in ChimeraX. I didn't know the recent version of the ConSurf server provided ChimeraX sessions, so that is helpful, thanks! You would have to talk to the ConSurf website developers about what information they put into the session. However, I would not expect it to have any Alphafold information (pLDDT or PAE values). It probably just has whatever atomic coordinates you uploaded (if that's how you input the structure), or atomic coordinates straight from the PDB. Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 26, 2024, at 8:04 PM, David S. Fay <DavidFay(a)uwyo.edu> wrote: > > Hi Elaine, > > I was able to open the ConSurf .cxs files using ChimeraX, which were part of the Consurf download. I have tried using ConSurf through Chimera or ChimeraX yet. I’ve attached an example image I recently obtained using ChimeraX. One limitation I haven’t worked is how to display PAE contacts between peptides when using this ConSurf file in ChimeraX. I can do it with AF2/3 files – no problem, but not with the ConSurf files. Also, the .cxs files don't seem to work for other ChimeraX functions, such as: hide @@bfactor<50 ribbon. It’s also unfortunate that ConSurf doesn’t allow you to visualize conservation for more than one of the two peptide chains, at least as far as I can tell. But it’s still quite useful. > > If you have any additional hints I’d be glad to try them. > > David > > > > <Screenshot 2024-07-26 at 8.54.04 PM.png> >> On Jul 26, 2024, at 3:11 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi David, >> Thanks for the info about the ConSurf website. Did you ever use the ConSurf website output in ChimeraX or were all the outputs only suitable for Chimera (which was my experience)? >> >> Some other notes, in case you or others didn't know... >> >> (1) ChimeraX also plots PAE data from AlphaFold2 or AlphaFold3 >> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#pae> >> >> example command: >> alphafold fetch LDLR_HUMAN pae true >> >> screenshot of result: >> <Screen Shot 2024-07-26 at 2.10.24 PM.png> >> >> (2) ChimeraX can convert mmCIF to PDB, i.e. you could just open the mmCIF file and then save the structure as PDB. Can be done with the File menu or with the commands "open" and "save": >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html> >> >> Elaine >> >>> On Jul 26, 2024, at 1:54 PM, David S. Fay via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> Real quick followup for those who might be interested. >>> >>> I did contact ConSurf. They suggested using a different browser and clearing the cache. I did both and it now works but only on Chrome and NOT on Safari (for those using Macs). This isn’t the first time I’ve had problems with Safari. ConSurf is helpful for looking at conservation of a protein sequence and/or a 3D structure. >>> >>> Incidentally, for converting cif to pdb, which is necessary for ConSurf, this site worked well. >>> https://project-gemmi.github.io/wasm/convert/cif2pdb.html >>> >>> Also, some may be interested in using this site to generate AF2-like red/blue PAE diagrams as well as creating spreadsheets of predicted peptide interactions from AF3. >>> https://predictomes.org/tools/af3/ >>> >>> David >>> >>>> On Jul 25, 2024, at 9:42 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>> >>>> ◆ This message was sent from a non-UWYO address. Please exercise caution when clicking links or opening attachments from external sources. >>>> >>>> >>>> Hi David, >>>> Did you try asking the Consurf developers? There is a "contact us" link on their website: >>>> >>>> <https://consurf.tau.ac.il/consurf_contact.php> >>>> >>>> I haven't used this web service recently. I have only used its outputs in Chimera so far (never ChimeraX). >>>> >>>> If I go to a page for precalculated results there is a "Chimera" download that gives a Chimera session (.py file), e.g. >>>> >>>> <https://consurfdb.tau.ac.il/main_output.php?pdb_ID=2GBP&view_chain=A&unique…> >>>> >>>> I tried downloading that just now, and it works in Chimera. In Chimera you can use File... Export Scene... and export a .py file that you can open with ChimeraX. Only the ribbon and carbon atoms are colored by the Consurf values, however, not the heteroatoms. >>>> >>>> I hope this helps, >>>> Elaine >>>> ----- >>>> Elaine C. Meng, Ph.D. >>>> UCSF Chimera(X) team >>>> Resource for Biocomputing, Visualization, and Informatics >>>> Department of Pharmaceutical Chemistry >>>> University of California, San Francisco >>>> >>>> >>>>> On Jul 24, 2024, at 8:08 PM, David S. Fay via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>>> >>>>> Hi, >>>>> >>>>> I’m curious if anyone else is having trouble getting results from ConSurf? The site appears to be up, which maybe wasn’t the case a while back. But trying various kinds of inputs doesn’t lead to any results. Rather, it just seems to just get hung up. (It’s also possible I’m doing something incorrectly.) >>>>> >>>>> Thanks in advance! >>>>> >>>>> David >>>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> >

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Doubt about volume cropping
by Leyre Marin Arraiza 29 Jul '24

29 Jul '24

Dear UCSF ChimeraX, I have a practical question regarding 3D volume visualization and cropping in ChimeraX. I have a big 3D density map which includes the densities for several models of different proteins. To facilitate visualization and model building, I would like to crop the density map, so that it includes only two of the models. Is it possible to crop my density map around those models, to make it a bit smaller and more focused on the areas of interest? Hope I am explaining myself. Thanks and best regards, Leyre Leyre Marin Arraiza PhD fellow University of Copenhagen Novo Nordisk Foundation Center for Protein Research Taylor Group Blegdamsvej 3B, Building 6, 6-1-10 2200 København N leyre.arraiza(a)cpr.ku.dk<mailto:leyre.arraiza@cpr.ku.dk> [CvwfJbQuv4S75bEAAAAASUVORK5CYII=] How we protect personal data<https://informationssikkerhed.ku.dk/english/protection-of-information-priva…>

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ChimeraX adjacent question about ConSurf
by David S. Fay 26 Jul '24

26 Jul '24

Hi, I’m curious if anyone else is having trouble getting results from ConSurf? The site appears to be up, which maybe wasn’t the case a while back. But trying various kinds of inputs doesn’t lead to any results. Rather, it just seems to just get hung up. (It’s also possible I’m doing something incorrectly.) Thanks in advance! David David S. Fay Ph.D. Professor, Department of Molecular Biology Associate Director, National Institutes of Health Wyoming INBRE University of Wyoming davidfay(a)uwyo.edu

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Question about Creating/Displaying Vectors
by John Watters 25 Jul '24

25 Jul '24

Hi All, I was wondering if anyone had any advice on how to make figures where vectors show the difference in the RMSD of the alpha carbons like in A/C here in ChimeraX: [https://iiif.elifesciences.org/lax/51898%2Felife-51898-fig3-v2.tif/full/617…] From this paper: https://elifesciences.org/articles/51898 [https://elifesciences.org/assets/images/social/icon-600x600@1.52e87ee6.png]<https://elifesciences.org/articles/51898> Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon–anticodon pairing<https://elifesciences.org/articles/51898> Chemical modifications near the tRNA anticodon and specific mRNA–tRNA pairs combine to control the ribosomal three-nucleotide mRNA reading frame, essential for the sequential addition of amino acids into polypeptide chains. elifesciences.org

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Re: combining and splitting chains
by Elaine Meng 25 Jul '24

25 Jul '24

Hi Dmitry, You can do the combining into one model with "combine" and the splitting into multiple models with "split", see links in my previous message. The "split" command can use residue ranges (not just chain IDs) so you can split it however you want even if it is one chain. However, I don't know if it makes sense to make it all one chain, but I think Eric already explained that part in his reply. The "changechains" command can change the chain ID, and "rename" can change the model name and ID: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html> I hope this helps, Elaine > On Jul 25, 2024, at 9:05 AM, Dmitry Semchonok <semchonok(a)gmail.com> wrote: > > Dear Elaine, > Thank you for your answer. > You were right. I meant to combine chains inside 1 model so that there would be only 1 model with 1 chain (instead of multiple). > Can we rename all of them to 1? > And vice versa — when there is one model, and one wants to split it into domains (chains)? > Any ideas? > Thank you. > Kind regards, > Dmitry > > Ps. Sorry, I can not send the emails with illustrations to ChimeraX somehow.From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: 22 July 2024 18:10 > To: Dmitry Semchonok <semchonok(a)gmail.com> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] combining and splitting chains > Hi Dmitry, > I thought you meant combining multiple chains into a single chain. However, if you instead meant combining chains that are in different models into a single model (still with multiple chains), see command "combine": > > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> > > Then if these chains have different chain IDs, it is easy to split that single model into multiple models again, one for each chain, with "split": > > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html> > > Regards, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Jul 20, 2024, at 3:50 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Hello Eric, > > Thank you for your answer. > > Following up combining and splitting chains topic I would like to specify more details. > > My question is connected to modelangelo output where one gets the separate chains. I would like to combine those chains in one structure. > > But maybe later I may need to divide the complete structure on chains again. > > Kind regards, > > DmitryFrom: Eric Pettersen <pett(a)cgl.ucsf.edu> > > Sent: 17 July 2024 19:26 > > To: Dmitry Semchonok <semchonok(a)gmail.com> > > Cc: ChimeraX <chimerax-users(a)cgl.ucsf.edu> > > Subject: Re: [chimerax-users] combining and splitting chains > > > > Hi Dmitry, > > You don't say why you want to combine/split these chains, so there might be more direct way to accomplish whatever your ultimate goal is than my answers below, if we knew what your goal was. > > You combine chains by using the 'bond' command (or Build Structure tool) to form the C→N bond (or O3'→P bond for nucleic acids) between the chains. ChimeraX will combine them into a single chain. > > Splitting chains is uglier because ChimeraX knows that the residues in a chain form a chain even if you delete connecting bonds or even entire residues. The recipe would be to open multiple copies of your model. In the first copy, in the chain you want to split delete everything but the first "segment" you want split off. In the second copy delete everything but the second segment (and all other chains if there are any). So on and so forth. Then use the "combine" command to combine the models into one. > > > > --Eric > > > > Eric Pettersen > > UCSF Computer Graphics Lab > > > >> On Jul 17, 2024, at 9:33 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > >> > >> Dear colleagues, > >> I have a lot of chains that I want to combine just in 1. > >> How to do that? > >> And vice versa – I have 1 chain, and I want to split it into several. > >> Thank you in advance, > >> Kind regards, > >> Dmitry

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Re: ChimeraX-SASA mismatch with contiguous sequences
by Elaine Meng 24 Jul '24

24 Jul '24

Dear Suhas, I hope your week is great as well, and we're glad you like ChimeraX! We recommend sending ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) unless they include private data. That way others can also answer, or benefit from the answers. In this case, it is explained in the "measure sasa" help. Please see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> The command measures the surface area *enclosing* the specified atoms. That is different than the surface area of those atoms in the context of the larger structure. So when you give two commands measuring two parts you also get more surface that goes around the ends of those parts. If you wanted the SASA in the context of the whole protein or whole chain, you would have to do it differently. As explained in the help link above, if you want to measure the SASA of those parts in the context of the whole protein chain's surface, it would instead be something like measure sasa /A sum /A:1-10 measure sasa /A sum /A:11-20 measure sasa /A sum /A:1-20 The Log gives: measure sasa /A sum /A:1-10Solvent accessible area for /A (2615 atoms) = 28035 Solvent accessible area for /A:1-10 (66 atoms) of /A (2615 atoms) = 1143 measure sasa /A sum /A:11-20Solvent accessible area for /A (2615 atoms) = 28035 Solvent accessible area for /A:11-20 (80 atoms) of /A (2615 atoms) = 427.09 measure sasa /A sum /A:1-20Solvent accessible area for /A (2615 atoms) = 28035 Solvent accessible area for /A:1-20 (146 atoms) of /A (2615 atoms) = 1570.1 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 23, 2024, at 11:59 PM, Suhas Srinivasan <suhas.srinivasan(a)stanford.edu> wrote: > > Dear Dr. Meng, > > Hope you are having a great week! > > Thank you for developing and maintaining ChimeraX as an essential analytical software for the community. > > We had a query since we noticed a discrepancy in the way SASA is reported. > If you were to consider the AlphaFold database structure for PCBP1 (Q15365) and perform the below SASA measurements, we noticed that: > SASA(1 to 10) + SASA(11 to 20) ≠ SASA(1 to 20) > > measure sasa /A:1-10 > Solvent accessible area for /A:1-10 (66 atoms) = 1385.3 > measure sasa /A:11-20 > Solvent accessible area for /A:11-20 (80 atoms) = 1632.6 > measure sasa /A:1-20 > Solvent accessible area for /A:1-20 (146 atoms) = 2850.8 > > There is a difference of ~167 sq. A. > It would be very helpful to understand why such a large difference exists when considering contiguous sequences of atoms/residues. > > ChimeraX-1.8 > macOS-14.5 (Intel) > > Thank you for your consideration. > > Kind regards, > Suhas Srinivasan

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Re: [Chimera-users] column selection: chimera vs chimeraX
by Eric Pettersen 23 Jul '24

23 Jul '24

Hi Mike, There wasn’t, but I just added code to do it. In tomorrow’s daily build (well, the next daily build that works :-) ) the alignment viewer’s context menu will have an “Expand Selection to Columns” entry that will do this. --Eric Eric Pettersen UCSF Computer Graphics Lab > On Jul 22, 2024, at 9:01 AM, 7mkf via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi there, > > I'm an avid user of chimera and have begun transitioning to chimeraX. A feature I find very useful in chimera is expand selection to columns within the multialignviewer. Is there a way to do this in ucsf chimeraX? > > Many thanks, > Mike > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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saving modifications
by Claudio Andres Aguilar Pena 23 Jul '24

23 Jul '24

Dear ChimeraX team, First of all, many thanks for the app, it’s really wonderful!. I have a question regarding one feature I would like to have and maybe it’s possible to do but I just don’t know how. I have a PDB of the structure of an enzyme that has 5 different domains: I can select the aa of each domain and give each domain a color. This is very useful for me when comparing structure predictions of the enzyme and see what happens when making mutations in the primary structure. My problem is that I cannot save the PDB with the colors for each domain, so I have to select and assign the colors every time, or leave the app and the PDB permanently open, which is not very convenient. Is there a way to save the PDB with the modifications I made? Many thanks for your help. Best, Claudio Dr. Claudio Aguilar, PhD Virologisches Institut Universität Zürich Vetsuisse Fakultät Winterthurerstrasse 266a CH-8057 Zürich Switzerland phone: +41446358712 Fax: +41446358911

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chimerax-0.1.71 python API: failed imports in module
by ishaanawasthi05＠gmail.com 22 Jul '24

22 Jul '24

Dear ChimeraX Team, I'm trying to use the ChimeraX API in python to automate some analysis. My code is not executing due to some missing/failed imports inside the ChimeraX module. File "/opt/anaconda3/lib/python3.11/site-packages/chimerax/core/models.py", line 54, in <module> from chimerax.graphics import Drawing, Pick, PickedTriangle ModuleNotFoundError: No module named 'chimerax.graphics' In the same file (models.py) there are also problems with this: "from .state import State" Together they are being used in the following class definition: class Model(State, Drawing): """ A Model is a :class:`.Drawing` together with an id number that allows it to be referenced in a typed command. .... """ I haven't been able to find any information on what these imports are, why they are missing, or how to resolve this issue. I also don't know if there are more missing imports, as it keeps failing here. I would appreciate your support in getting the Chimerax API to work — if this is the wrong place to ask, please do point me toward the right forum for ChimeraX. Thanks so much for the help!

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combining and splitting chains
by Dmitry Semchonok 22 Jul '24

22 Jul '24

Dear colleagues, I have a lot of chains that I want to combine just in 1. How to do that? And vice versa – I have 1 chain, and I want to split it into several. Thank you in advance, Kind regards, Dmitry

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ChimeraX journal-quality figures script !
by Gupta, Arun 22 Jul '24

22 Jul '24

Dear ChimeraX team, Recently, I came across this review article “Front. Microbiol.13, 2022, 891610” and I am quite fascinated by the visually appealing figures made in the above-mentioned review article. Since the figures were created with UCSF ChimeraX in the review article. I was just wondering can somebody advice or suggest what should be the specific ChimeraX command scripts for making similar journal-quality figures. Find attached one of the example figures from the review article for the reference. Thanks! Arun

3 2

Chimerax on Fedora 40
by Vito Calderone 19 Jul '24

19 Jul '24

I have installed ucsf-chimerax-1.8-1.el9.x86_64.rpm on a fedora 40 pc. Installation was fine. When I launch 'chimerax' I get the following error: $ chimerax Fatal Python error: Segmentation fault Current thread 0x00001500f588ab80 (most recent call first): File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed File "<frozen importlib._bootstrap_external>", line 1233 in create_module File "<frozen importlib._bootstrap>", line 573 in module_from_spec File "<frozen importlib._bootstrap>", line 676 in _load_unlocked File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 1176 in _find_and_load File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/Qt/QtWebEngineWidgets.py", line 4 in <module> File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed File "<frozen importlib._bootstrap_external>", line 940 in exec_module File "<frozen importlib._bootstrap>", line 690 in _load_unlocked File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 1176 in _find_and_load File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed File "<frozen importlib._bootstrap>", line 1232 in _handle_fromlist File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/Qt/__init__.py", line 112 in qt_have_web_engine File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 108 in __init__ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 653 in init File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in <module> File "<frozen runpy>", line 88 in _run_code File "<frozen runpy>", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._p cg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets (total: 18) Segmentation fault (core dumped) Any hint? Thanks Vito -- Dr. Vito Calderone Ph.D. Associate Professor of Inorganic Chemistry CERM and Department of Chemistry University of Florence Via Luigi Sacconi, 6 50019 Sesto Fiorentino (FI) Italy tel: +39 055 457 4276

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sequence identity command
by NUR AIDA SAKINAH 18 Jul '24

18 Jul '24

Hai, I want to use the sequence identity command in ChimeraX but in the log said "Missing or invalid "src1" argument: Expected alignment-id or [alignment-id]:sequence-name-or-number". The input I gave is "sequence identity alignment-1" after open the tools>sequence>show sequence viewer and then select model e.g. #1/a and it show the ID as [ID: 1] but i got error. How to solve this problem? Hope ChimeraX teams can help. Thank you!

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